[gmx-users] RE: MPI runs on a local computer

2013-09-20 Thread Xu, Jianqing
...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Xu, Jianqing Sent: 19 September 2013 13:49 To: gmx-users@gromacs.org Subject: [gmx-users] MPI runs on a local computer Dear all, I am learning the parallelization issues from the instructions on Gromacs website. I guess I got a

[gmx-users] MPI runs on a local computer

2013-09-19 Thread Xu, Jianqing
Dear all, I am learning the parallelization issues from the instructions on Gromacs website. I guess I got a rough understanding of MPI, thread-MPI, OpenMP. But I hope to get some advice about a correct way to run jobs. Say I have a local desktop having 16 cores. If I just want to run jobs on

RE: [gmx-users] Gromacs on Intel Xeon and AMD Opteron

2013-09-11 Thread Xu, Jianqing
ubject: Re: [gmx-users] Gromacs on Intel Xeon and AMD Opteron Hmm, that looks like a problem. Which GROMACS version, and which compiler version? (See mdrun -version) On Wed, Sep 11, 2013 at 3:06 PM, Xu, Jianqing wrote: > > Thanks for the comments, Mark. > > Sorry that I did not exp

RE: [gmx-users] Gromacs on Intel Xeon and AMD Opteron

2013-09-11 Thread Xu, Jianqing
r way you must expect differences. MD simulations are chaotic. However, the long-time ensemble averages should agree well - that's the point of the simulation. Mark On Wed, Sep 11, 2013 at 10:35 AM, Xu, Jianqing wrote: > Dear all, > > This is my first time here. I apologize if I am

[gmx-users] Gromacs on Intel Xeon and AMD Opteron

2013-09-11 Thread Xu, Jianqing
Dear all, This is my first time here. I apologize if I am not aware any rules for posting a new message. I was testing Gromacs on two servers, one server has AMD Opteron processor (Server 1), and the other has Intel Xeon processor (Server 2). The simulation system that I tried is the lysozyme